A jury on Friday found the meek monsignor too loyal for his own good, convicting him of a felony for refusing to challenge his cardinal and stop the cover-up of child sex abuse by priests.

Lynn’s conviction is the first for a U.S. church official and comes in a diocese now beset by layoffs, parish closures and a new round of soul searching over the long-running abuse scandal.

“Why does this stand out? Because he didn’t say no,” said the Rev. Chris Walsh, a city pastor who leads the Association of Philadelphia Priests, an independent group formed last year to gather support and information for rank-and-file priests.

Lynn’s conviction comes the weekend some Philadelphia parishes are celebrating their final Masses before closing for good and priests are saying goodbye before their traditional June transfers. Meanwhile, the archdiocese is cutting 45 jobs to help close a $17 million deficit, which it calls unrelated to legal bills that hit $10 million this fiscal year, not even counting most of Lynn’s trial costs.

Lynn, 61, is spending his first weekend in custody. He faces 3 1/2 to 7 years in prison on the endangerment charge.

His case shines light on the culture of obedience ingrained in Catholics, especially priests. Archdiocesan priests in Philadelphia take vows of obedience to their archbishop, and trial testimony demonstrated that Cardinal Anthony Bevilacqua treated a priest whistle-blower more harshly than some priest abusers.

“You don’t say no to Cardinal Bevilacqua,” Monsignor James Beisel said last month when he testified as a defense witness.

The trial shows the need for renewed debate about the relationship between obedience and conscience, one Catholic academic said.

“The Catholic church hierarchy certainly thinks there’s too much discussion in the U.S. about conscience, that people use it to justify any kind of proclivity,” said Mathew Schmalz, a religious studies professor at the College of the Holy Cross in Worcester, Massachusetts. “But in this case, there are some really deep issues about when do you stand up to the actions of those superiors.”

Lynn, after a stint as a seminary dean, was hand-picked by Bevilacqua for the secretary for clergy’s office in 1991. He spent a year as an understudy before becoming secretary in June 1992. He soon learned the job involved more than priest assignments and routine personnel matters.

There also was the matter of the secret church archives containing child sexual abuse complaints lodged over the years against Philadelphia priests. There were hundreds of them, dating to the 1940s. And more than 100 priests, many of them still active, were accused.

Bevilacqua wanted Lynn to spearhead the complaints.

“I never asked for an assignment, and I never asked out of one,” Lynn testified.

By his own account, Lynn was an adept bureaucrat. He was organized. He was hardworking. And he was discreet.

Lynn and his assistant, Beisel, set out to gauge the scope of the problem. They took to the task each night for about two weeks, using passcodes to enter the locked room near the golden-domed Basilica of Saints Peter and Paul that housed the secret files. Beisel couldn’t stand it. Given the late hour, he just wanted to hurry up and get home, he testified.

Nonetheless, they compiled a 15-page list of names and sex acts, noting whether the priests were diagnosed pedophiles or presumed guilty based on their own admissions. They also noted whether the statute of limitations had run for legal action.

A version of that list became a smoking gun at trial. The list went missing for more than a decade. Lynn told a grand jury about it in 2004 but said he couldn’t find it. A copy that had been stashed in a locked, long-abandoned safe surfaced at the archdiocese days after Bevilacqua’s death in January. So, too, did a 1994 memo that shows Bevilacqua ordering Lynn’s supervisors to shred all copies of the list.

Many institutions try to protect their reputations, but shredding documents takes it to a new level, Schmalz said.

“Shredding documents — especially with Watergate and all this history we have of institutional malfeasance — does have a symbolic significance that goes beyond the view of the Catholic church as being closed and insular,” he said. “So it is shocking to think what must have gone on leading up to that decision.”

The task fell to Monsignor James Molloy, who died in 2006. But Bishop Joseph R. Cistone signed off as witnessing the list’s destruction. He now leads the diocese of Saginaw, Michigan. Neither he nor retired Allentown Bishop Edward Cullen, Bevilacqua’s top aide, was called to testify.

Nor did they come to Lynn’s defense. Few, if any, church officials have stepped forward to share in the blame for the sex abuse scandal, even though District Attorney Seth Williams said Friday that many have “dirty hands.”

Walsh said: “The cardinal could have done that a year ago, two years ago, and obviously Bishop Cullen and Bishop Cistone could still do it.”

Beisel, overwhelmed by the clergy office job, quit after a year. Lynn stayed for more than a decade. But he was the rare aide to Bevilacqua who was never made a bishop.

By 2004, Bevilacqua had retired, the clergy sexual abuse scandal had erupted in Boston, and a grand jury investigation was under way in Philadelphia. U.S. bishops had adopted a zero tolerance policy for accused priests. And new diocesan panels were being formed to handle abuse complaints, with varying degrees of success.

It was time for Lynn to move on. Submissive to the end, he said he declined to request his next assignment. Instead, he accepted a desirable posting as pastor of a large, upscale parish in suburban Downingtown. He was put on leave after his arrest last year. Loyal parishioners from the parish, St. Joseph’s, sometimes attended his trial.

A spokesman for Voice of the Faithful, a Boston-based group formed in the wake of the abuse crisis to try to empower lay Catholics, said it was “obvious that here’s this one man sitting (on trial) when there should be scores of people sitting there.”

“The moral call to stand when you’re guilty and confess seems to have been abrogated by those in power. It was, ‘I’m just following orders,”’ spokesman Nick Ingala said. “The organization that claims to be the moral authority in the world has given up that moral authority.”